Zhan Xiong

Zhan Xiong, Junling He, Pieter Valkema et al.

Renal biopsies are the gold standard for the diagnosis of kidney diseases. Lesion scores made by renal pathologists are semi-quantitative and exhibit high inter-observer variability. Automating lesion classification within segmented anatomical structures can provide decision support in quantification analysis, thereby reducing inter-observer variability. Nevertheless, classifying lesions in regions-of-interest (ROIs) is clinically challenging due to (a) a large amount of densely packed anatomical objects, (b) class imbalance across different compartments (at least 3), (c) significant variation in size and shape of anatomical objects and (d) the presence of multi-label lesions per anatomical structure. Existing models cannot address these complexities in an efficient and generic manner. This paper presents an analysis for a \textbf{generalized solution} to datasets from various sources (pathology departments) with different types of lesions. Our approach utilizes two sub-networks: dense instance segmentation and lesion classification. We introduce \textbf{DiffRegFormer}, an end-to-end dense instance segmentation sub-network designed for multi-class, multi-scale objects within ROIs. Combining diffusion models, transformers, and RCNNs, DiffRegFormer {is a computational-friendly framework that can efficiently recognize over 500 objects across three anatomical classes, i.e., glomeruli, tubuli, and arteries, within ROIs.} In a dataset of 303 ROIs from 148 Jones' silver-stained renal Whole Slide Images (WSIs), our approach outperforms previous methods, achieving an Average Precision of 52.1\% (detection) and 46.8\% (segmentation). Moreover, our lesion classification sub-network achieves 89.2\% precision and 64.6\% recall on 21889 object patches out of the 303 ROIs. Lastly, our model demonstrates direct domain transfer to PAS-stained renal WSIs without fine-tuning.

Chunlin Ji, Hanchu Shen, Zhan Xiong et al.

Generalized zero shot learning (GZSL) is still a technical challenge of deep learning as it has to recognize both source and target classes without data from target classes. To preserve the semantic relation between source and target classes when only trained with data from source classes, we address the quantification of the knowledge transfer and semantic relation from an information-theoretic viewpoint. To this end, we follow the prototypical model and format the variables of concern as a probability vector. Leveraging on the proposed probability vector representation, the information measurement such as mutual information and entropy, can be effectively evaluated with simple closed forms. We discuss the choice of common embedding space and distance function when using the prototypical model. Then We propose three information-theoretic loss functions for deterministic GZSL model: a mutual information loss to bridge seen data and target classes; an uncertainty-aware entropy constraint loss to prevent overfitting when using seen data to learn the embedding of target classes; a semantic preserving cross entropy loss to preserve the semantic relation when mapping the semantic representations to the common space. Simulation shows that, as a deterministic model, our proposed method obtains state of the art results on GZSL benchmark datasets. We achieve 21%-64% improvements over the baseline model -- deep calibration network (DCN) and for the first time demonstrate a deterministic model can perform as well as generative ones. Moreover, our proposed model is compatible with generative models. Simulation studies show that by incorporating with f-CLSWGAN, we obtain comparable results compared with advanced generative models.